Transcript levels in mouse liver
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Utham Valekunja
PROVIDER: E-GEOD-37387 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Total RNA was isolated from liver samples of C57/BL6 mice over a circadian time course, 3 biological replicate samples per time point were collected and processed individually. RNA from each individual biological replicate sample was extracted using RNeasy mini kit (Qiagen Cat# 74106) and hybridized on an Affymetrix mouse Gene ST1.0 microarray.
2013-01-01 | GSE37387 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-01-01 | E-GEOD-37396 | biostudies-arrayexpress
Project description:Ovarian cancer is a deadly gynecological malignancy for which novel biomarkers and therapeutic targets are imperative for improving survival. To investigate the role of histone H1 in ovarian cancer cells, we overexpress a histone H1 variant, H1.3, in the OVCAR-3 epithelial ovarian cancer cell line. RNA was extracted from OV-3/H1.3(H) cells (OVCAR-3 with overexpression of H1.3) and control cells of OVCAR-3 transfected with vectors without H1.3. The microarray chip used was human Affymetrix ST1.0 array. Gene expression changes caused by overexpression of H1.3 in OVCAR-3 cells were identified. Affymetrix Human Exon 1.0 ST array was used to identify the changes in transcriptome of OVCAR-3 caused by overexpression of H1.3
2014-10-31 | E-GEOD-61692 | biostudies-arrayexpress
Project description:This study determined the genes that are differetially expressed when regulatory T cells were stimulated in vitro with IL-2 388 Affymetrix targets were found to be up or down regulated in human regulatory T cells by IL-2 by two-fold or more. Gene enrichment analyss identified that IL-2 functions to regulate gene expression for mRNAs important for immune system processes, cell growth, cell death, inflammatory response, cell migration, and the Jak/Stat pathway, among others. A subset of these differentially expressed genes were distinctively expressed between individual subjects. Human regulatory T cells (Tregs) cells were FACS purified based on expression of CD4+ CD127-lo CD25-HI. These cells were cultured for 24 hr in media with or without IL-2 (100 u/ml). The cells were harvested, total RNA was prepared and processed to probe Affymetrix human Gene ST1.0 arrays.
2015-07-09 | E-GEOD-49817 | biostudies-arrayexpress
Project description:Much is known concerning the cellular and molecular basis for CD8+ T memory immune responses. Nevertheless, conditions that selectively support memory generation have remained elusive. Here we show that an immunization regimen that delivers TCR signals through a defined antigenic peptide, inflammatory signals through LPS, and growth and differentiation signals through the IL-2R initially favors antigen-specific CD8+ T cells to rapidly and substantially develop into tissue-residing T effector-memory cells by TCR transgenic OVA-specific OT-I CD8+ T cells. Amplified CD8+ T memory development depends upon a critical frequency of antigen-specific T cells and direct responsiveness to IL-2. A homologous prime-boost immunization protocol with transiently enhanced IL-2R signaling in normal mice led to persistent polyclonal antigen-specific CD8+ T cells that supported protective immunity to Listeria monocytogenes. These results identify a general approach for amplified T memory development that may be useful to optimize vaccines aimed at generating robust cell-mediated immunity. Gene expression analysis was performed for OT-I T cells on day 3 and day 5 after activation with ovalbumin and LPS in vivo with and without treatment with IL-2 using an agonists IL-2/anti-IL-2 complexes (IL2/Jes-6.1) OT-I T cells were purified and adoptively transferred into congenic syngenic mice. 24 hours later mice were immunization with ovalbumin and LPS. 24 hr later some mice received agonist IL2/anti-IL2. 3 and 5 days after immunization, the activated OT-I T cells were purifed by FACS and total RNA was isolated for genome wide expression analysis using Affymetrix Mouse Gene ST1.0 arrays
2012-10-03 | E-GEOD-39110 | biostudies-arrayexpress
Project description:Daily (circadian) clocks are essential for regulating and coordinating physiology in mammals. Modulation of local chromatin structure has been shown for only a small number of genes, principally thought to be directly modulated by Clock-mediated histone acetylation. Here we show that genome-wide changes of active and suppressive histone marks control global chromatin architecture over the day and night. Examination of mouse liver tissue at 4 time-points around the clock in "free-running", continuous conditions (constant darkness, temperature and food available ad libitum).
2013-01-08 | E-GEOD-23550 | biostudies-arrayexpress
Project description:How proliferative and inhibitory cell signals integrate to control liver regeneration remains poorly understood. A screen for antiproliferative factors repressed after liver injury identified Tob1, a member of the PC3/BTG1 family of mitoinhibitory molecules as a target for further evaluation. Tob1 protein decreases after 2/3 hepatectomy in mice secondary to post-transcriptional mechanisms. Deletion of Tob1 increases hepatocyte proliferation and accelerates restoration of liver mass after hepatectomy. Down-regulation of Tob1 is required for normal liver regeneration and Tob1 controls hepatocyte proliferation in a dose-dependent fashion. Tob1 associates directly with both Caf1 and the Cyclin/cdk complex to modulate kinase activity. In addition, Tob1 has significant effects on the transcription of critical cell cycle components, including E2F targets and genes involved in p53 signaling. These studies provide direct evidence that levels of an inhibitory factor control the rate of liver regeneration. Our data identify Tob1 as a crucial check-point molecule that acts by by modulating levels and activity of cell cycle proteins. Samples from wild type and Tob1 null mice as normal adults and 24 hours after 2/3 hepatectomy are used. Each experimental point used data from two chips, each having a different set of three pooled animals. In summary we had 8 chips: 2 for WT time 0, 2 for WT time 24, 2 for KO time 0, 2 for KO time 24.
2010-05-28 | E-GEOD-21836 | biostudies-arrayexpress
Project description:Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum, mock-infected, or uninfected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae. Experiment Overall Design: Total RNA was purified from pooled intact zebrafish larvae (31-82 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols. Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (30ug/replicate) were fragmented using standard methods. Hybridization and scanning were performed using standard Affymetrix protocol. Raw expression values were normalized (Invariant set method) and modeled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).
2008-06-16 | E-GEOD-8327 | biostudies-arrayexpress
Project description:Male Fischer rats were fed a control diet or a diet supplemented with 50, 500 or 1000 ppm Phenobarbital. The 500 and 1000 ppm PB doses induced a transient hyperplasia and a sustained hepatomegaly in treated animals. The animals were sacrificed and liver miRNAome was profiled in three animals per group after 1, 3, 7, and 14 days of treatment. The aim was to investigate the time and dose dependent effects of phenobarbital treatment on the liver miRNAome Three animals were profiled from control or each treatment group after 1, 3, 7, and 14 days
2013-07-03 | E-GEOD-48489 | biostudies-arrayexpress
Project description:We investigated the combined sensitivity of micro-flow liquid chromatography with a ZenoTOF mass spectrometer for high throughput proteomic and phosphoproteomic analysis of rat tissues. Comparing the proteomes acquired using data-independent acquisition (DIA) on the ZenoTOF 7600 with the previous generation TripleTOF 6600, more proteins were quantified using a fifth of the sample load and a third of the instrument time. Zeno SWATH data was evaluated using replicate injections of rat organ digests to compare FragPipe and DIA-NN computational pipelines. FragPipe identified more proteins in 7 of the 8 rat organs, with an extra 12% and 17% observed in heart and muscle tissue respectively. The number of identified peptides per protein were higher with FragPipe and the precision of missing values across replicate injections was more consistent. Single-shot phosphopeptide enrichment from 100 µg rat tissue, without fractionation, was acquired using data-dependent acquisition (DDA) on both instruments. A total of 5,108 phosphosites were quantified with a negligible increase in phosphosites found using the ZenoTOF 7600 relative to the 6600. Using DIA on the ZenoTOF, 8,013 phosphosites were quantified using Spectronaut.
2024-06-02 | PXD045472 | Pride